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- PDB-2pku: Solution structure of PICK1 PDZ in complex with the carboxyl tail... -

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Basic information

Entry
Database: PDB / ID: 2pku
TitleSolution structure of PICK1 PDZ in complex with the carboxyl tail peptide of GluR2
Components
  • PRKCA-binding protein
  • peptide (GLU)(SER)(VAL)(LYS)(ILE)
KeywordsPROTEIN BINDING / PROTEIN COMPLEX
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation ...G protein-coupled glutamate receptor binding / membrane curvature sensor activity / postsynaptic endocytic zone / postsynaptic early endosome / glial cell development / cellular response to decreased oxygen levels / Arp2/3 complex binding / postsynaptic specialization / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / monoamine transport / dopamine transport / SNAP receptor activity / protein kinase C-activating G protein-coupled receptor signaling pathway / dendritic spine organization / regulation of postsynaptic neurotransmitter receptor internalization / long-term synaptic depression / dendritic spine maintenance / receptor clustering / Trafficking of GluR2-containing AMPA receptors / regulation of insulin secretion / positive regulation of receptor internalization / protein targeting / cellular response to glucose starvation / ionotropic glutamate receptor binding / cytoskeletal protein binding / ephrin receptor binding / protein kinase C binding / trans-Golgi network membrane / G protein-coupled receptor binding / phospholipid binding / intracellular protein transport / receptor tyrosine kinase binding / actin filament binding / synaptic vesicle / GTPase binding / presynaptic membrane / dendritic spine / postsynaptic density / cytoskeleton / neuron projection / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / protein phosphorylation / dendrite / glutamatergic synapse / synapse / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / mitochondrion / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain ...PICK1, BAR domain / Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / AH/BAR domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PRKCA-binding protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPan, L. / Wu, H. / Shen, C. / Shi, Y. / Xia, J. / Zhang, M.
CitationJournal: Embo J. / Year: 2007
Title: Clustering and synaptic targeting of PICK1 requires direct interaction between the PDZ domain and lipid membranes
Authors: Pan, L. / Wu, H. / Shen, C. / Shi, Y. / Jin, W. / Xia, J. / Zhang, M.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRKCA-binding protein
B: peptide (GLU)(SER)(VAL)(LYS)(ILE)


Theoretical massNumber of molelcules
Total (without water)9,7312
Polymers9,7312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PRKCA-binding protein / Protein kinase C-alpha-binding protein / Protein interacting with C kinase 1


Mass: 9155.532 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EP80
#2: Protein/peptide peptide (GLU)(SER)(VAL)(LYS)(ILE)


Mass: 575.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the peptide was chemically synthesized

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1213D 13C-separated NOESY
1312D NOESY

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Sample preparation

DetailsContents: 1mM 15N, 13C protein sample; 50mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 30 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.refinement
CYANA2.1P.GUNTERT ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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